Package picard.sam
Class SortSam
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.SortSam
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@DocumentedFeature public class SortSam extends CommandLineProgram
Sorts a SAM or BAM file.Summary
This tool sorts the input SAM or BAM file by coordinate, queryname (QNAME), or some other property of the SAM record. The SortOrder of a SAM/BAM file is found in the SAM file header tag labeled SO.For a coordinate sorted SAM/BAM file, read alignments are sorted first by the reference sequence name (RNAME) field using the reference sequence dictionary tag labeled SQ. Alignments within these subgroups are secondarily sorted using the left-most mapping position of the read (POS). Subsequent to this sorting scheme, alignments are listed arbitrarily.
For queryname-sorted alignments, the tool orders records deterministically by queryname field followed by record strand orientation flag, primary record flag, and secondary alignment flag. (SeeSAMRecordQueryNameComparator.compare(SAMRecord, SAMRecord)
} for details). This ordering may change in the future.Inputs
- Input BAM or SAM file to sort
- Sorted BAM or SAM output file
- Sort order of output file
Usage example:
java -jar picard.jar SortSam \ INPUT=input.bam \ OUTPUT=sorted.bam \ SORT_ORDER=coordinate
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Field Summary
Fields Modifier and Type Field Description File
INPUT
File
OUTPUT
picard.sam.SortSam.SortOrder
SORT_ORDER
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description SortSam()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(doc="The SAM, BAM or CRAM file to sort.", shortName="I") public File INPUT
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OUTPUT
@Argument(doc="The sorted SAM, BAM or CRAM output file. ", shortName="O") public File OUTPUT
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SORT_ORDER
@Argument(shortName="SO", doc="Sort order of output file. ") public picard.sam.SortSam.SortOrder SORT_ORDER
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Method Detail
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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